This study investigates the physical controls to hydrologic exchange and heat exchange in a large lowland river at different scales. Through a combination of field experiments and modeling, this work addressed two ecologically-relevant scales in the San Joaquin River, CA: the riffle-pool scale (150 m) and the longitudinal scale (240 km).

At the riffle-pool scale, in situ measurements of hydraulic conductivity (ksat) were collected over the length of two riffles, interstitial pore water temperatures were measured within artificial redds, and near-bed temperatures were obtained using 2 km of fiber optic cable and distributed temperature sensing (DTS). These data were used to inform a two-dimensional numerical model of subsurface flow and temperature in gravel bars. Asymmetry of bar morphology is a first-order control to the extent and magnitude of infiltration, which is greater at low flow than high flow. Hydraulic conductivity varies by orders of magnitude and systematic downstream coarsening arises related to the process of bar genesis. The lowest values of ksat were observed where the difference between the topographic gradient and the water surface gradient is at a maximum and thus where the infiltration would be greatest into a uniform bar.

Morphology and fine sediment accumulation in recharge zones exert an important control over the mechanisms driving subsurface heat exchange. Conduction dominates heat exchange when infiltration fluxes are ≤ 0.4 -- 0.9 m/d-1 and depends on sediment grain size. A ksat value of approximately 135 -- 300 m/d-1 is required for advection-dominated exchange.

At the longitudinal river scale, a spectral energy balance model was developed, assessed, and used without calibration to investigate the fluvial and hydroclimatological controls to the energy balance over the length of a river during a large-scale flow experiment. Absorbed shortwave radiation is the dominant heat flux and is controlled by changes in sediment, depth, and streamwise patterns in velocity which drive the advective exchange. Downstream variation in sediment results in a 20 percent change to total absorbed radiation and the relationship between net absorption and streambed sediment albedo is shown to be linear. During periods of low flow, up to 45 percent of absorption occurs at the bed.